Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

Cell type

Cell type Class
Breast
Cell type
Breast cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
Breast cancer PDX HCI-005 tumour
tissue
PDX model HCI-005
time point
Short-term (5 days treatment)
chip antibody
ERα (HC-20)X (Santa Cruz SC-543X)
treatment
DHT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tumors were cut into 30µm slices on a cryostat and fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 5.5 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with ERα antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction. Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495). ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
102415955
Reads aligned (%)
77.4
Duplicates removed (%)
7.3
Number of peaks
6831 (qval < 1E-05)

hg19

Number of total reads
102415955
Reads aligned (%)
76.7
Duplicates removed (%)
8.9
Number of peaks
6183 (qval < 1E-05)

Base call quality data from DBCLS SRA